Shadows From The Past
by NN010
Summary: AU: Skye is an ARGUS agent and was on Lian Yu for a year before ARGUS found her and recruited her, she was on an undercover assignment in The Rising Tide hacker group when SHIELD found her while she was searching a building and her past starts to catch up with her. Full character list inside. Chapter release schedule running on Valve Time...
1. Present Day Prologue

Author's Note: This is another new story from me, yeah I'm not doing so good when it comes to updating my other stories but this one is one idea I want to get up. This is an AU Agents of SHIELD, Arrow crossover with a bit of The Flash in there as well. The opening bit of this prologue is in medias res (basically the story starts in the middle and goes back to the beginning to show what led to that point).

Here are all of the main and recurring characters:

SHIELD:

The original six (Phil Coulson, Skye, Melinda May, Grant Ward, Leo Fitz, and Jemma Simmons (all except Skye in present day only), all 6 are main characters with Skye being the protagonist),

And SHIELD Director Nick Fury (Present Day only, recurring character).

Arrow:

Slade Wilson/Deathstroke (Present Day and Flashbacks, main character and Main Antagonist),

Lyla Michaels (Present day only, recurring character)

Oliver Queen (Flashbacks only, main character),

Sara Lance (Flashbacks only, recurring character),

And ARGUS Director Amanda Waller (Present day only, recurring character).

The Flash:

Barry Allen (Present day only, recurring character),

Joe West (Present day only, recurring character),

And Iris West (Present day only, recurring character).

Oh and Skye in this story is a bit like Oliver Queen but without the biological family (at the moment but at the in medias res portion she knows but they aren't mentioned by name to prevent spoilers)

Present Day Prologue: Skye was in the middle of a fight with Slade Wilson/Deathstroke, she thought he died 10 years ago but he didn't die and he was plotting his revenge. Skye was wearing an outfit reminiscent of The Arrow (she was called "Dark Arrow" (not to be confused with "The Dark Archer", that's Malcolm Merlyn), Slade was wearing an Iron suit reminiscent of an evil version of Iron Man without the helmet/mask. Right before Skye could fire an Arrow and end their fight Slade punched her and everything went black, causing her to look back upon what led her to that point.

It all started 6 months earlier when she was surveying a building that she planned on searching as Dark Arrow later that day, Skye was wearing civilian clothing to blend in, Skye at that point was undercover inside The Rising Tide for ARGUS, the organization that acts as a group of men and women who take on the missions that other organizations like SHIELD, the FBI, and CIA can't handle, the reason Skye was under was to use them as a smoke screen and take down Centipede and The Clairvoyant from the shadows. Right before she was going to leave, the building blew up and shortly after a hooded man jumped out of the building with a woman in his arms.

THE END FOR NOW!


	2. Present Day Chapter 1

Author's Note: I'm glad to see so many people give this story a chance (102 as of when this was uploaded) as I definitely had a good title right off the bat, it's a better start than my last story "Agents of Lyoko Season 1" or "Code: SHEILD Season 1" as it used to be called, and there aren't too many "Skye's undercover inside the original team" stories out there (I know there's also "The Bracelet" (bad title for a good story) by Jimmy 144 in the normal Agents of S.H.I.E.L.D. fandom and "New Skys" by Pebna Wolf which is an Agents of S.H.I.E.L.D./Avengers crossover). The way I'm writing this story is that "Present Day Chapter insert chapter number here" means the chapter is set in present day, "Flashback Chapter insert chapter number here" means it's a Flashback to Skye's time on Lian Yu, and "Chapter insert chapter number here" means it's both. I plan on going heavily AU in this story, Skye being under is just the beginning of the AU stuff that's going to happen. Also here are my personal thoughts on the 2 hour Agents of S.H.I.E.L.D. Season 2 finale "SOS" and the Arrow season 3 finale "My Name is Oliver Queen", the former was an amazing, action packed, WTF finale (Can't wait to see Skye's superhero team/Black Ops Task Force), and the latter was an action packed disappointment that could have been way better (I'm worried about Arrow Season 4 now).

Present Day Chapter 1: Hunting For Answers: As "The Hooded Hero" put down the woman in his arms he looked right into Skye's eyes and ran away right after, Skye had luckily recorded the whole thing and planned to post the video online when she got back to her van before searching for and talking to the hero, after that she would put on her "Dark Arrow" costume and search the building in front of her at that moment in time, hopefully before S.H.I.E.L.D. and/or Centipede cover it all up. With a plan in mind she left for her van, which doubled as her base of operations, ARGUS hooked her up with when she went under. When she got back she edited and posted her video of The Hooded Hero on the internet and then called Lyla Michaels, her handler of sorts and mother figure.

"Agent Skye, update log 21, it's been 3 months since my last update and it has been a busy 3 months, between all the brief relationship stuff between me and Miles, hacking into S.H.I.E.L.D. twice, searching for answers about my past, fighting Centipede, and just today recording footage of "The Hooded Hero" I've been quite busy and haven't had the time to do something like this." Skye started with.

"It's alright Skye, I get it, you were busy, what have you found on Centipede over the last 3 months?" Lyla asked Skye.

"It seems that Centipede had a lab here in LA before it was destroyed and The Hooded Hero jumped out of it, he may be using their Centipede Serum, you know, the one with Extremis, the Mirakuru serum that Slade had in him that drove him mad to the rate where I had to kill him, traces of Erskine's Super Soldier Serum used on Steve Rogers, and Gamma Radiation all in one." Skye answered.

"So what's your plan?" Lyla asked.

"I plan on talking to him today and convincing him to go public and then search the lab for any useful Intel on the Centipede Group." Skye answered.

"Now that that's over with, how are things with your step-family?" Lyla asked.

"You know the rules; you have to tell me about how things are going with Dig!" Skye responded.

"Alright Skye you win, Johnny and I are still dating, hoping things go better than our last marriage. Now will you tell me about how things are going with Joe?" Lyla responded.

"Alright, I visited Central City last week, Barry and Iris clearly have romantic feelings for each other but neither of them know how to express them. Joe was being praised by Captain Singh as usual, and The Mardon Brothers were in town and I kind of helped Joe attempt to take them down but they escaped, don't worry I was in my Dark Arrow costume when doing so. Also did you just call Dig Johnny?!" Skye finally answered while also expressing shock.

"Your damn right I did! Now you can go find that Hooded Hero." Lyla then hung up.

"Alright, so off to finding The Hooded Hero, all you have to do is talk to him and not kill him like you did with Slade Wilson nearly 10 years ago, no pressure." Skye muttered to herself, she then proceeded to sit at a bus stop for a few minutes and then found her man, she followed him into a restaurant and sat at the same table as him, she also noticed that the guy is job hunting.

"Just act natural." Skye told him.

"What?" The man asked.

"Just pretend that we're talking." Skye answered.

"We are?" the man asked confused.

"Good, because you never know who's listening." Skye answered, looking around to make sure no one was listening, especially S.H.I.E.L.D, The Rising Tide, and/or Centipede, it was natural instinct due to being undercover for a couple years.

"I don't even know who the hell's talking." the guy responded.

"I'm Skye, and you're The Hooded Hero. Please for the loves of god don't tell me you're staying with that name." Skye introduced herself.

"Wait, what? I'm not- I'm a factory worker." The guy responded, 'He's trying to throw me off his scent, well I know he's jacked up on Centipede's super soldier serum, and he's a terrible liar', Skye thought to herself.

"You're a terrible liar. Sure, by day you are. I saw you, you're a hero. Like a for-real superhero which is- not that I'm a groupie stalker type or anything but that's so cool! Alright just chill and don't draw attention... you're in danger." Skye responded.

"You've got the wrong guy, Skye." The guy responded.

"You're lying again, and you've got the wrong approach, you're a superhero, potentially an Avenger if you get yourself that far and you can't even find a job." Skye convinced him.

"I guess it's useless to lie to you. What kind of danger were you talking about earlier?" the man asked.

"S.H.I.E.L.D." Skye responded.

"Shield, I should carry a shield?" the man asked.

"S.H.I.E.L.D; Government, scary men in dark suits who come after guys like you. They knew about The Battle of New York and The Starling City Undertaking before either of those even happened, and cleaned them up, overnight, before any REAL questions could be asked, like 'How did Malcolm Merlyn get his hands on an Earthquake machine'. How long do you think it will take them to clean YOU up?" Skye asked him.

"And YOU want to know why I'm hiding." The man responded.

"What if you didn't hide? What if you got in front of this and let the world know that you're a hero? That should be easy because that video of you saving that girl is the most popular internet video since that cat that had vertigo and said girl is dying to thank you! Also a guy like that gets work, gets perks. I can help, I'm great with computers, and I can help you get a whole new identity or even, a mask!" Skye responded.

"Okay..." The guy stood up and got ready to leave.

"Or we could just stay with the hood. Listen if you change your mind you can stop by my office-" Skye explained as she pick pocketed his driver's license.

"You have an office?" The guy asked.

" Yes, a mobile office, it's a van, I live in a van, by choice, it's always in that alley back there, I have free Wi-Fi, and you can come anytime." Skye told him.

"It was nice talking to you Skye, but I've gotta go." The man responded before leaving.

"They're coming for you! Mike." Skye yelled out before muttering the last part to herself. She went back to the van and put on her Dark Arrow costume and went onto the rooftops and ran to the Centipede lab that blew up earlier that day, 'I have a few minutes before S.H.I.E.L.D. comes here, gotta be quick but through.' Skye thought to herself. She used an explosive arrow to blow the door open, the door was fused to the frame due to the explosion, 'That's weird' Skye thought to herself. She searched the room and found a security Camera; she plugged it into her phone and copied the data over. Suddenly she heard footsteps coming in, 'S.H.I.E.L.D.' Skye thought. She turned around, readied an arrow and raised her bow, and found 2 scientists, Skye lowered the bow, a mistake as another agent snuck up behind her and knocked her out. She woke up to find herself in a holding cell of sorts made of Vibranium, Agent Coulson walked in, 'Wait, I heard he died shortly before The Battle of New York, and I haven't seen him for 3 years' Skye thought to herself.

"Long time no see Skye, I just need to ask you a few questions." Coulson started.

THE END FOR NOW


	3. Present Day Chapter 2

Author's Note: As you saw last chapter, Coulson and Skye have history with each other, that history will be explained this chapter, I will do the first flashback chapter after I have finished this universe's version of SHIELD 1x01, the flashbacks will jump forwards and backwards in time, I will indicate this at the start of that chapter. Plus I have downgraded the rating of this story from M to T and the flashbacks occurred 10 years prior to the main story.

Present Day Chapter 2: Interrogation With a Ghost: Still shell-shocked about Coulson, one of her dearest friends and one of the only people inside S.H.I.E.L.D. that she trusts, she asked

"Coulson, How the hell are you alive?" with raw emotion heavy in her voice, she knew that the other agents from the lab were listening.

"I was never truly dead, I was only dead for 50 seconds, Fury faked my death so that The Avengers could band together to save the world from The Chitauri. After that I had a stay in Tahiti for a few weeks and I got this plane and team as tokens of good will. Anyways off to my first question, what were you of all people doing at the rubble of a blown up lab?" Coulson answered then asked.

"Well… I've been undercover in The Rising Tide for the past 2 years; I've been using them as a cover to take down Centipede." Skye answered.

"Next question, what is Centipede?" Coulson asked.

"Wait a minute; you don't know what Centipede is? –Sigh- I'll tell you, only because I figured S.H.I.E.L.D. would have known about Centipede by now and you guys are only going to get more entangled in their business anyway. Centipede is some kind of terrorist organization hell bent on creating their own super soldier serum, by combining every known source of powers into one serum, Extremis, Mirakuru, Gamma Radiation, hell, even Erskine's serum all into one super serum. I'm no scientist but I know from fighting prior users of this serum that it has the explosive issues of Extremis, the emotionally instability issues of Mirakuru, and that users must be injected with the serum on a regular basis, without the serum their just men, at least, according to an analysis of the serum done by my step-brother, Central City Police Department Forensic Scientist Barry Allen, he did it because of 2 reasons,

Because he has always been interested and believed in "The Impossible".

Because he is smarter than any scientist A.R.G.U.S. has." Skye answered.

"Final question: Do you still trust me?" Coulson asked.

"You know I do, Phil, especially after what happened during my brief time at S.H.I.E.L.D., but Bahrain and Wakanda were proof that I was more of an A.R.G.U.S. agent than a S.H.I.E.L.D. agent." Skye answered without a second thought and she unwillingly flashed back to Wakanda.

"After this whole thing with The Hooded hero is over, would you consider giving us a second chance, as a Consultant?" Coulson asked.

"After 'You Know What' happened in Wakanda? You know that S.H.I.E.L.D. won't exactly welcome me back with open arms." Skye responded.

"Just answer the question, Skye." Coulson sighed.

"Alright, I'll do it, but I've been trying to keep the killing to a minimum though, so keep that in mind." Skye answered.

"I'll bear that in mind." Coulson reassured.

THE END FOR NOW

Author's Note 2: So this was a quieter expositional chapter on Coulson and Skye's past working relationship, next chapter will return to the main narrative. Also feel free to speculate what happened in Wakanda that caused Skye to leave S.H.I.E.L.D. and return to A.R.G.U.S.!


	4. Present Day Chapter 3

Author's Note: This chapter will be a long one, probably won't get back to the main narrative (sorry), and will reuse the interrogation scene from "Hunting for Answers" and "Interrogation with a Ghost". Don't worry Skye will not be as dark and brooding as Oliver, she's like a mix of her canon self and Oliver Queen.

Present Day Chapter 3: Learning the Truth:

While Agent May and FitzSimmons were investigating the rubble of the lab (and capturing Skye, unbeknownst to Coulson and Ward), Coulson and Ward were moving in to capture their mysterious hacker, they found her van, only to find it devoid of any human life.

"Whoever in The Rising Tide hacked S.H.I.E.L.D. must have learned we were onto them and left in a hurry." Ward assumed.

"No… this is an A.R.G.U.S. issued van, whoever hacked us must have been undercover in The Rising Tide." Coulson deduced, his phone then vibrated in his pocket, the caller ID read 'Melinda May'.

"Hello May, have FitzSimmons found anything in that lab yet?" Coulson asked.

"That's why I called, they found a surveillance camera, a strange looking device that might be an 0-8-4, and your old friend, former S.H.I.E.L.D. agent, and A.R.G.U.S. agent Skye AKA Dark Arrow in that lab, she was searching it, I managed to knock her out while FitzSimmons were unknowingly distracting her and we're on our way back to The Bus right now." May answered.

"Ward and I will head back right now." Coulson replied before hanging up. After a half hour of driving they were back on The Bus (a black heavily modified airplane officially designated S.H.I.E.L.D. 616 that Coulson's Team were using as their base of operations, Coulson got it as compensation for Loki stabbing him).

"Who is she?" Ward and FitzSimmons asked simultaneously.

"Luckily our command center can access S.H.I.E.L.D., A.R.G.U.S., FBI, CIA, and NSA data bases or else I wouldn't be able to explain to you." Coulson explained before pulling up Skye's A.R.G.U.S. file.

"A.R.G.U.S. Agent Skye, real name unknown, also known by her codename Dark Arrow, biological family is also unknown, she has been searching for them her whole life, she has a step-family in Central City, her step father, Joe West, is a detective for the CCPD, her step sister, Iris West, is an employee at Jitters and aspires to be a journalist, and her step brother, Barry Allen is an assistant forensic scientist for the CCPD who spends his spare time looking into anything he thinks will connect to his mother's murder, "The Impossible" in essence, basically what we'll be looking into on a regular basis, the police believe his father killed her, but he testifies time and time again that a man in yellow killed her, S.H.I.E.L.D. believes him and has placed this mysterious Man in Yellow on The Index as he is believed to have super speed. Skye spent some time 10 years ago on an island in the North China Sea called Lian Yu, which literally is Chinese for Purgatory Island. According to this she was trained by Slade Joseph Wilson, due to this training she can withstand Chinese Water Torture for 7 minutes –everyone bar Coulson was shocked-, he ended up crossing her after the death of his love interest Shado, he seems to pin the blame on her, Skye killed him by putting an arrow through his eye after he threatened to take away everything and everyone she cared about. She also worked for S.H.I.E.L.D. for a time after A.R.G.U.S. brought her to Hong Kong and she, Oliver Queen, he was on the island with her and was also brought to Hong Kong, and a couple others stopped the U.S. Army's attempt to cripple China with the Alpha-Omega bio weapon, but left to return to A.R.G.U.S. after a mission in Wakanda, there aren't any known reports on what happened there and she would have my head if I told you." Coulson explained.

"She has seen a lot of darkness over the past 10 years." Fitz realised.

"Yes she has Fitz, now I'm going to go in there and talk to her, give her a friendly and familiar face to talk to." Coulson told them before heading to 'The Cage' as they were calling it, the team watched through security footage.

"Long time no see Skye, I just need to ask you a few questions." Coulson started.

"Are you sure this will work?" Ward muttered to May.

"I have faith in him." May replied.

"Coulson, how the hell are you alive?" Skye asked, raw emotion heavy in her voice.

"I was never truly dead, I was only dead for 50 seconds, Fury faked my death so The Avengers would band together to save the world from The Chitauri. After that I had a stay in Tahiti for a few weeks and got this plane and team as a token of good will. Anyways, off to my first question, what were you of all people doing at the rubble of a blown up lab?" Coulson answered then asked.

"He actually was dead for only 8 seconds, Hill said so and that it gets longer every time he tells it, he told me he was dead for 40 seconds, for instance." Ward explained.

"Well… I've been undercover in The Rising Tide for the past 2 years, I've been using them as a smoke screen to take down Centipede." Skye answered Coulson's question.

"WHAT THE HELL IS CENTIPEDE?!" May, Ward, Fitz, and Simmons all exclaimed at once.

"Next question, what is Centipede?" Coulson asked.

"Thank god he's asking that." Simmons sighed in relief.

"Wait a minute; you don't know what Centipede is? –Sigh- I'll tell you, only because I figured you would have known about Centipede by now and you guys are only going to get more entangled in their business anyway. Centipede is some kind of terrorist organization hell bent on creating their own super soldier serum, by combining every known source of powers into one serum, Extremis, Mirakuru, Gamma Radiation, hell, even Erskine's serum all into one super serum. I'm no scientist but I know from fighting prior users of this serum that it has the explosive issues of Extremis, the emotionally instability issues of Mirakuru, and that users must be injected with the serum on a regular basis, without the serum their just men, at least, according to an analysis of the serum done by my step brother, Central City Police Department Forensic Scientist Barry Allen, he did because of 2 reasons,

Because he has always been interested and believed in 'The Impossible'.

Because he is smarter than any scientist A.R.G.U.S. has." Skye answered.

"So that's what Centipede is… but what the hell is Mirakuru?" Fitz thought out loud before letting his confusion out.

"Final question, do you still trust me?" Coulson asked Skye.

"You know I do, Phil, especially after what happened during my brief time at S.H.I.E.L.D; but Bahrain and Wakanda were proof that I was more of an A.R.G.U.S. agent than a S.H.I.E.L.D. agent." Skye answered without a second thought.

"After this whole thing with The Hooded Hero is over, would you consider giving us a second chance?" Coulson asked Skye.

"After 'You Know What' happened in Wakanda? You know that S.H.I.E.L.D. won't exactly welcome me back with open arms." Skye responded. Coulson sighed before saying,

"Just answer the question, Skye."

"Alright, I'll do it, but I've been trying to keep the killing to a minimum though so keep that in mind." Skye answered.

"I'll bear that in mind. Sorry but I have a couple burning questions in my head that need answering before leaving this room, who is 'The Hooded Hero' and did you hack into S.H.I.E.L.D. in order to maintain your cover?" Coulson reassured then asked.

"To answer your questions, Mike Peterson, you check my pockets for his ID if you need to be sure, and yes, the first time it was to search for info on my family, like when I snuck into the records library at The Hub to search for the same thing and like when I did that I found nothing, the other times were to help maintain my cover, like when I released the location of that Chitauri neural link, I hated every time I had to release S.H.I.E.L.D. secrets." Skye answered.

"She just admitted to have leaked that Chitauri neural link, I could have died because of her 'Undercover Operation'!" Ward exclaimed.

"But she did say she hated doing it!" Simmons defended.

"Whatever..." Ward sighed.

"Alright Skye, we're done here." Coulson told Skye as he opened the door.

"Good and can any of you get these cuffs off, they're tight as hell!" Skye exclaimed, Ward then removed the handcuffs once she was out.

"Skye, right? What is Mirakuru?" Fitz asked.

Skye sighed, "Mirakuru was the Japanese attempt to recreate Erskine's super solider serum. It almost worked, but it didn't, the flaws with the serum are that it causes bleeding from the eyes upon injection, if it doesn't consider you 'Worthy' you die, and if it does it will cause physical or psychological deterioration, Slade Wilson is an example of the mental deterioration. Oliver and I injected him with the serum, but it drove him mad and after Shado died, it also seems to cause hallucinations of the person the user misses most and said hallucinations tell them to commit horrible actions in their name, Slade seems to suffer from this as every bad thing he has done to me was in Shado's name." Skye explained. Then Coulson put on a news report on a factory incident that had just occurred, the team realized it involved Mike Peterson/The Hooded Hero.

"Alright, time to look up Mike Peterson." Skye muttered.

"Mike Peterson, factory worker, has one kid, and he's divorced, the poor guy got injured and then got laid off his previous job, good guy, bad breaks, then one day someone…" Coulson explained before getting cut off.

"Debbie Muller, Centipede's American recruiter, she runs their operations here, a woman named Raina recruited her into Centipede a few years ago, she must have recruited Mike, gave him the Centipede serum and swore him into secrecy." Skye realized.

"Fitz what do we have from the security footage Skye uploaded to her phone from before the blast?" Coulson asked, Fitz then pulled up the footage.

"Well the man is angry at the other man." Fitz answered.

"The data is very corrupt." Simmons explained.

"Yeah, like Cold War Russia corrupt!" Fitz exclaimed.

"I-I can't sync the timecode without…" Fitz continued before being cut off.

"What if you had the audio? I obviously have picked up some excellent knowledge of computers over the past couple years. I was running surveillance on the lab due to it being a Centipede lab, I had my shotgun mic pointed at the window before the blast. If I get my van back into that alley, then I'm back in business. But there's too much background noise for me but you could probably-" Skye offered before Simmons cut her off, they talked for a bit.

"Um, that audio would be great. Thank you very, very much." Fitz accepted.

"We will take that audio, please." Simmons accepted at the same time.

"Skye, you'll go with May to that alley and send that audio our way and Fitz will figure out what happened in that lab, Simmons will be doing a breakdown of that serum to see there's anything Barry missed." Coulson told Skye.

"It would be my pleasure to do so." Skye responded.

THE END FOR NOW!


	5. Present Day Chapter 4

Author's Note: Sorry for not updating sooner, writer's block kicked in for a while and I started a SYOC spinoff called The Blacklist (check it out, though it is chronologically a few months ahead of this). The title of this chapter will make sense at the end. Just so you know this story's overall plot line will be a mix of Agents of S.H.I.E.L.D season 1 and Arrow season 2, there will be a few OC's being added to the team soon, some submitted and others from my own imagination and one of the ones from my head is going to admittedly be playing the role Skye did in canon though even then there will be twists to fit the darker tone of this series compared to the MCU and some other multi story AOS fanfics as this story is the first of a planned trilogy. Also starting this chapter there will be certain present day chapters that will be written directly from Skye/Dark Arrow's POV, all flashback chapters will be written from Skye's POV, If the first person thing is well received I will write all future chapters of this trilogy in first person, also Skye's 'Dark Arrow' persona was my own creation, not something pulled from anything Marvel or DC have done in the past as far as I know. I also plan a West family one shot series with Joe, Barry, Iris, and Skye at various points in their lives.

Off Topic: I recently have seen "Jurassic World" and I thought it was a great movie. Only problem being that some supporting characters (particularly Vincent D' Onofrio's Ingen representative) felt like cartoon characters, though the Indominus Rex was a force to be reckoned with and Chris Pratt was being Chris Pratt!

DISCLAIMER: I don't own anything here but this story.

Present Day Chapter 4: About to Blow(Skye POV chapter): As May and I traveled in my van to the back alley which had been my base of operations for the past 2 years, May asked some questions so she could know how much I had changed in the past 3 years.

"Does it bother you, killing all those people, I mean, I killed 1 gifted child and her parent back in Bahrain, you know that because you were there, but to kill all the people you've killed, torture numerous people, and still joke around afterwards like you do?" Agent Melinda 'The Calvary' May asked me (not that I would EVER dare to call her The Calvary).

"Well… the fact is, what I do requires conviction, nerves of steel, a killer instinct, and the will to do the hard thing, even if it's not pretty or if you don't want to. So I wouldn't be who I am today if it did, or I'd probably be dead. We've arrived at our destination." I answered before announcing our arrival. I then got to work on sending the audio files to Fitz and the team, which I was starting to consider myself a part of, though I still have to take down Centipede and find and kill or capture The Clairvoyant who's behind the whole thing, depending on who it is.

"That should do it!" I exclaimed as I closed my laptop after a few minutes, I proceeded to grab 2 SD cards, one that contained everything I had on Centipede and another that had everything I had on my past, which was basically my admission form to St. Agnes Orphanage and my adoption papers from when Joe decided to adapt me while on vacation in New York City. Then I saw Mike come out of nowhere and knock May out cold.

"Mike, what are you doing here?" I asked, 'He can't know I'm an agent of both ARGUS and SHIELD' I thought to myself.

"Saving you, from the scary men in the dark suits, and you're going to save us." Mike answered, 'Us, what does he mean by us?' I thought to myself. I proceeded to ask him that question; he then brought forward a child.

"Alright, stay strong for me Ace ('So that's the child's name' I thought to myself), because the nice lady ('He's referring to me' I thought to myself) will help us get a new life, we'll take a train, we might even take the nice lady with us ('SHIT' I mentally exclaimed while hiding the fear from my face), but regardless we'll make it through this because what are we?" Mike reassured then asked his son Ace.

"We're a team!" Ace answered before fist bumping his father, Mike then told me to drive to Union Station, when he told me, I saw a hint of orange on his face 'The Extremis part of the Centipede Serum is still unstable and is on the verge of blowing'.

THE END FOR NOW!


	6. Present Day Chapter 5

**Author's Note: SORRY FOR RUNNING ON VALVE TIME FOR THIS CHAPTER (Valve Time being when someone says they'll release something on one date then releases it much, much later)! If this were a TV show, this chapter would be the end of the present day portion of the pilot while the flashbacks will be inter cut between the present day stuff. I will start writing that way when I start adapting Episode 2 of both shows.** **Also sorry for taking so long with this chapter, I got Tom Clancy's The Division, Batman: Arkham Knight, Batman: The Telltale Series (Episode 1 and 2, titled Realm of Shadows and Children of Arkham respectively (playing Children of Arkham tonight)) Rise of The Tomb Raider, Metal Gear Solid V: The Phantom Pain, Call of Duty: Black Ops III, Bloodborne, both Fallout 4 and New Vegas, both Battlefield 4 and Battlefield: Hardline, Halo 5: Guardians,. Lego Marvel's Avengers, Overwatch, Mass Effect 1, and Dishonoured recently and between those games and more (and getting addicted to some of them (*cough* Fallout 4, Fallout New Vegas, Rainbow Six Siege, and The Division *cough*), Agents of SHIELD (Great third season (I did cry when I saw the "A Spy's Goodbye" scene from "Parting Shot" and I'm liking Quake vs. Ghost Rider), keep mind Daisy Johnson is NOT Skye in this fic), Arrow (meh** **season 4 (I dropped Arrow after 4X18))** **, The Flash (Great** **season 2, cliffhanger has me worried about season 3 though), and Daredevil (stopped watching after episode 6)** **all coming back, checking out Blindspot (Great show, Greg Berlanti who helped created Arrow, The Flash, and Legends of Tomorrow) is an executive producer on this show), The Muppets (relatively funny show though I lost interest after 3 episodes), Minority Report (the show was a stinker, disappointing considering how great the film was), Jessica Jones (Personally thought it was better than Daredevil, would recommend it to anyone who likes the Netflix corner of the MCU, psychological thrillers, character studies, and/or great storytelling) and Designated Survivor (Great pilot episode, really want to know who's behind the attack), seeing Civil War (thought it was great, I was really surprised by the way things turned out) and life I've been busy lately. This Chapter Mike will take his son Ace and a captive Skye to Union Station to get on a train but Coulson's Team will try to stop him from getting away and losing his mind. Also I don't have a beta so any mistakes are my own. This fic is also available on AO3 (the first present day chapter is up now and the first flashback chapter should be cross posted here and on AO3 in the next month after that I'll post both the remaining present day chapters to get it caught up and cross posting flashback chapters, I'm planning on posting chapters once or twice a month alongside my AOS/Flash fic, The Blacklist, and my take on an AOS High School AU (more info coming soon). I'm on Tumblr now, link is in my profile bio, you'll want to follow me there as I'm using it to keep you guys posted on fic progress! Sorry for the excruciatingly long author's note (It was 1 and a half pages in my Word document for this chapter), here's the long overdue chapter!**

Present Day Chapter 5: Union Station: A half hour after Mike had knocked May out cold and took me hostage. Skye had gotten them to Union Station.

"Come on Skye, do your thing!" Mike exclaimed, 'He's talking about hacking into the internet and removing all traces of him from the web, the look in his eyes say it all. I'll do it but not without leaving a trace of my location so the team can come and hopefully save Mike from himself' Skye thought to herself. With a plan mapped out in the cold, manipulative, lethal, and highly trained assassin part of her mind, Skye started putting it into action, starting with hacking into the bus, it only took her 5 minutes (because she knew SHIELD's firewall like her P226 and was skipping her usual encryption protocols on purpose) and the team hopefully had her location, after that she started hacking into the California district database to erase all traces of Michael and Ace Peterson, when 30 minutes had passed Mike was clearly impatient and might have been contemplating getting someone else to do the job instead.

"COME ON SKYE! What's taking you so long?!" Mike was clearly fuming with anger and out of patience.

"Damnit Mike, it's not like in the movies where this can be done in ten minutes! I'm bypassing the California state firewall so I can delete every single trace of Michael and Ace Peterson on the web. This stuff takes a while damnit!" Skye responded to Mike's rather unstable attitude. Mike was about to head out of the van when someone knocked on the door.

"MR. PETERSON! WE KNOW YOU'RE IN THERE! COME OUT AND WE CAN HELP YOU!" Coulson, who was presumably using a megaphone, offered to Mike. He didn't take the offering well…

"What happened?! Did you tell them our location?" Mike yelled at Skye.

"No, I must have forgotten to encrypt our location because you were RUSHING ME!" Skye yelled at him in turn 'he is really getting on my nerves' Skye thought to herself. While Skye was in her train of thought Mike burst the van's right side door open, taking Ace with him. She grabbed her gun from her hidden compartment under her driver's seat, holstered it behind her back, feeling the metal brush with her lower back and then walked over to Coulson.

"So what's the plan Coulson? I'm thinking we should try to contain the situation, kill him if neces-'' Skye starts before Coulson cuts her off.

"We'll contain the situation, but don't kill him; I'm not letting a kid lose his father today!" Coulson told her in response. Then a "cop" cocked his Beretta 92FS and aimed it at Skye. May then pushed Skye out of the way, right when he pulled the trigger, the bullet grazed her in the arm, but as a legendary field agent, May barely felt the bullet.

"Someone really wants you dead!" Coulson observed.

"Must be Centipede, I've been the pain in their ass over the last couple years, of course they would want me dead!" Skye guessed. 'The British scientist', as Skye called Simmons in her head at the time due to not getting her name, gave her a rifle that looked unlike anything she had seen before.

"The Night-Night gun is non-lethal, should allow you to neutralize Mike in a way that he'll survive." Fitz explained to her. 'Night-Night gun is a dumb name, sounds like a name they got from a kid or something' Skye thought to herself when she heard the name.

"Yeah as long as he survives the 200 hundred foot drop…" Skye mumbled to herself before she went into the station and began to line up her shot. Her ears told her someone was trying to sneak up on her (and not doing it well), she subsequently went into fight mode and hit the "cop" with the butt of her tranquilizer gun (she refused to refer to it by its real name, even in her head), she then threw the gun to the side, not giving a damn about the fact that it was probably one of a kind, and used the strength of the man as he tried to punch her to twist his arm, proceeding to kick his right leg before punching him in the back of his head, instantly knocking him out. She went back and grabbed the gun and resumed trying to line up her shot when she saw another Centipede goon shoot Mike in the shoulder, causing him to fall to the ground, during his fall Skye decided to take cover behind a stand that was a short distance away. Coulson was walking towards him; he put his gun (a Smith and Wesson pistol) down on the ground, probably as a show of faith.

"Do you really think that this changes anything? I know how this works!" Mike responded, clearly not taking the whole thing well.

"I don't. I really don't know if you'll explode or if you're just going to drop dead. But regardless of what happens, we'll make sure your son is safe." Coulson told him, that was all he could say before Skye sniped him with her tranq rifle (there was no way she was gonna call it the "Night-Night Gun"). That afternoon they gave Mike to SHIELD to let him decide his own fate and they sent Ace to his aunt's and told him his dad will be okay.

"I told him his father will be coming home soon, even though I don't know when he's coming home…" Skye told Coulson.

"So you're sure you want to be SHIELD Agent Skye West instead of ARGUS Agent Skye West/Dark Arrow?" Coulson asked Skye.

"I'm sure; I kind of need a change of pace, no promises that I won't be the one with the highest body count a few months from now though." Skye answered.

"Are you still looking for your real parents Skye?" Coulson asked her as they stepped into Lola (Coulson's corvette).

"Haven't had the chance to go looking much in recent months but I am." Skye answered again. Coulson's phone rang.

"Sir, we have a 0-8-4." Ward told them.

"Is that confirmed?" Coulson asked.

"They want us to go in and confirm it." Ward responded.

"We'll be there in 10 minutes." Coulson told him.

"One more thing, Fury sent us another agent, she said her name was Carmen Fowler." Ward notified Coulson.

"Maybe you should introduce us when we get back." Skye responded.

"Thanks for the heads up." Coulson acknowledged.

"So does she still fly?" Skye asked Coulson about Lola. Coulson switched the car into hover flying mode which answered Skye's question.

"Seems that the tide is rising." Coulson quipped.

"Too soon Coulson." Skye responded.


	7. Flashback Prologue

Author's Note: So here is the first flashback chapter, with a longer wait than I originally planned (and I forgot to post it simultaneously with the AO3 version) and sorry it's so short! Those AOS high school AU's and my AOS/Flash fic are still coming (I'm hoping to get the high school AU's out very soon!), I just wanted one more Shadows from the Past chapter out before beginning those! Also if you want to keep up to date on the progress of my various fics follow me at NN010 on Tumblr (if you guys want me to do a similar "I'll update you on WIP fics" deal on another social media platform let me know!)

Flashback Prologue: Crash: Skye was on a plane headed for Hong Kong, believing she would at least find clues on who her biological parents are. Suddenly there was some thunder and next thing she knew the wings hit and the plane was going down. "All passengers this is your pilot speaking we are" the pilot announced before being cut off by a pair of gunshots that killed the pilots. The PA system then cut out. As the plane continued circling Skye thought her life was over. Then it all faded to black.

The Following Morning: Skye woke up finding herself having washed up ashore on a strange island. 'Great, I've been washed up on an island all Cast Away style. Except I don't even have any cargo from the plane nearby to use, I'll be dead in days' Skye thought to herself. She heard gunshots 'So I'm not alone here, maybe I'll survive longer than a few days, or I'll be dead in minutes'.

THE END FOR NOW!


	8. Update and Upcoming Rewrite

Sorry for the long hiatus. So the plan going forward is to do away with the flashbacks unless necessary to the plot. I've taken so long to post because of my lack of interest in the flashbacks. So, yeah, rewrite incoming.


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